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- EMDB-2380: Structure of herpesvirus fusion glycoprotein B-bilayer complex re... -

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Basic information

Entry
Database: EMDB / ID: EMD-2380
TitleStructure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction
Map dataSubtomogram average of HSV-1 glycoprotein B bound to a lipid bilayer
Sample
  • Sample: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
  • Protein or peptide: Envelope glycoprotein B
Keywordselectron cryo microscopy / tomography / membrane proximal region / protein coat / pseudo-atomic / modelling / virus-host interaction
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsMaurer UE / Zeev-Ben-Mordehai Z / Pandurangan AP / Cairns TM / Hannah BP / Whitbeck JC / Eisenberg RJ / Cohen GH / Topf M / Huiskonen JT / Grunewald K
CitationJournal: Structure / Year: 2013
Title: The structure of herpesvirus fusion glycoprotein B-bilayer complex reveals the protein-membrane and lateral protein-protein interaction.
Authors: Ulrike E Maurer / Tzviya Zeev-Ben-Mordehai / Arun Prasad Pandurangan / Tina M Cairns / Brian P Hannah / J Charles Whitbeck / Roselyn J Eisenberg / Gary H Cohen / Maya Topf / Juha T Huiskonen / Kay Grünewald /
Abstract: Glycoprotein B (gB) is a key component of the complex herpesvirus fusion machinery. We studied membrane interaction of two gB ectodomain forms and present an electron cryotomography structure of the ...Glycoprotein B (gB) is a key component of the complex herpesvirus fusion machinery. We studied membrane interaction of two gB ectodomain forms and present an electron cryotomography structure of the gB-bilayer complex. The two forms differed in presence or absence of the membrane proximal region (MPR) but showed an overall similar trimeric shape. The presence of the MPR impeded interaction with liposomes. In contrast, the MPR-lacking form interacted efficiently with liposomes. Lateral interaction resulted in coat formation on the membranes. The structure revealed that interaction of gB with membranes was mediated by the fusion loops and limited to the outer membrane leaflet. The observed intrinsic propensity of gB to cluster on membranes indicates an additional role of gB in driving the fusion process forward beyond the transient fusion pore opening and subsequently leading to fusion pore expansion.
History
DepositionMay 21, 2013-
Header (metadata) releaseJun 26, 2013-
Map releaseJul 31, 2013-
UpdateAug 21, 2013-
Current statusAug 21, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bom
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bom
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2380.png

Downloads & links

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Map

FileDownload / File: emd_2380.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of HSV-1 glycoprotein B bound to a lipid bilayer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.6 Å/pix.
x 100 pix.
= 460. Å		4.6 Å/pix.
x 100 pix.
= 460. Å		4.6 Å/pix.
x 100 pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-12.513064379999999 - 18.673780440000002
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.64.64.6
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z460.000460.000460.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-12.51318.6740.000

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Supplemental data

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Sample components

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Entire : HSV-1 glycoprotein B ectodomain lacking the membrane-proximal reg...

EntireName: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
Components
  • Sample: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
  • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1000: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal reg...

SupramoleculeName: HSV-1 glycoprotein B ectodomain lacking the membrane-proximal region bound to a lipid bilayer
type: sample / ID: 1000 / Oligomeric state: One trimer of gB bound to a lipid bilayer / Number unique components: 2
Molecular weightExperimental: 259 KDa / Theoretical: 235 KDa
Method: Weights are for the trimeric ectodomain lacking the membrane proximal region. The experimental weight was determined by mass spectrometry. The theoretical weight was calculated from the sequence.

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Name.synonym: gB-1, gB1
Details: Liposomes consisting of phosphatidylcholine and cholesterol at 1.7:1 molar ratio were incubated with gB at pH 5.5 at 37C for one hour
Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1) / Strain: stain KOS / synonym: Human herpes simplex virus 1
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pCW289
SequenceUniProtKB: Envelope glycoprotein B / GO: symbiont entry into host cell / InterPro: Herpesvirus Glycoprotein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 5.5 / Details: PBS with sodium citrate
GridDetails: Cflat
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber temperature: 120 K / Instrument: OTHER / Method: Blot manually for 3 s before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 17, 2008
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 9 / Average electron dose: 100 e/Å2
Details: The dataset consists of 9 tomograms (containing 38 liposomes with bound gB). Data were binned by factor of 2.
Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 67000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder: liquid nitrogen cooled / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe sub-tomograms were picked manually from tomographic reconstructions of 38 liposomes
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Jsubtomo
Details: The best 786 spikes (of 996) were selected based on constrained cross correlation coefficient and by excluding overlaps. All three Euler angles of the spike were refined.
Number subtomograms used: 996
CTF correctionDetails: Low pass filter to the first zero crossing of the CTF

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Atomic model buiding 1

Initial modelPDB ID:

3nwf


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-4bom:
Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction

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